Wednesday, 17 September 2008

Weekly BioNews 8 - 15 Sep 2008

Emerging cryopreservation techniques are increasing hope of restoring fertility for women after diseases such as ovarian cancer that lead to destruction of reproductive tissue. The same techniques can also be used to maintain stocks of farm animals, and protect against extinction of endangered animal species by maintaining banks of ovarian tissue or even nascent embryos that can used to produce offspring at some point in the future.

Until now these clearly related fields of research concerning preservation of animal and human ovarian tissue have been largely separate, but are now coming together to reinforce each other, following a highly successful workshop on cryopreservation of ovarian tissue, organised by the European Science Foundation (ESF). The human and animals cryopreservation fields have much to teach each other, and progress in both is likely to be accelerated as a result of growing collaboration, according to the ESF workshop's convenor Claus Yding Andersen.

Both parties can learn from each other," said Andersen. "Experiments which cannot be performed in women can be done in animal species," he noted, pointing out that much of the progress in humans has come as a result of animal experiments. But it is in humans where most successful transplantations of frozen ovarian tissue after thawing have been carried out, and where greatest experience in the field has been gained. Therefore the ESF conference considered how this could be applied to conservation of endangered species. "The vast experience in women, with several children born as a result of transplantation of frozen/thawed ovarian tissue, can be applied in endangered species to know where to implant and how to obtain pregnancies," said Andersen. The techniques will also be valuable in agriculture, for preserving ovaries of farm animals in tissue banks with the potential for subsequent re-creation...

Oil spills and other environmental pollution, including low level leaks from underground pipes and storage tanks, could be quickly and easily spotted in the future using colour coded bacteria, scientists heard today (Thursday 11 September 2008) at the Society for General Microbiology's Autumn meeting being held this week at Trinity College, Dublin.

"Because bacteria have simple single-celled bodies it is relatively easy to equip them with a sensor and a brightly coloured 'reporter protein' which shows up under a microscope, alerting us to different substances leaking into the soil or seawater from oil spills, agricultural chemicals or other pollutants," says Professor Jan Van der Meer from the University of Lausanne in Switzerland.

Scientists have successfully shown that living bacteria can be used as a much more environmentally friendly way of detecting pollution than the currently used chemical methods of working out what has happened. "Chemical methods are often cumbersome, require sophisticated equipment, costly reagents or nasty materials," says Professor Van der Meer. "In comparison, our sensing bacteria are very simple to maintain. Tests with the bacteria are therefore extremely easy to carry out and do not require noxious chemicals."

"Our own tests, and checks by other laboratories, have shown that pollution testing using bacteria is a remarkably robust technique and produces reliable results," says Professor Van der Meer. "The heart of our colour sensor system is the bacteria themselves. They reproduce themselves in a growth medium, which makes the whole set-up really cheap,"

The new technique has already been successfully tested during a research expedition at sea, when the scientists demonstrated that the bacteria could measure different chemicals seeping from oil into the water, showing up as the blue light of bioluminescence in a simple light recording device...

Scientists have developed nanometer-sized 'cargo ships' that can sail throughout the body via the bloodstream without immediate detection from the body's immune radar system and ferry their cargo of anti-cancer drugs and markers into tumors that might otherwise go untreated or undetected.

In a forthcoming issue of the Germany-based chemistry journal Angewandte Chemie, scientists at UC San Diego, UC Santa Barbara and MIT report that their nano-cargo-ship system integrates therapeutic and diagnostic functions into a single device that avoids rapid removal by the body's natural immune system. Their paper is now accessible in an early online version at:

"The idea involves encapsulating imaging agents and drugs into a protective 'mother ship' that evades the natural processes that normally would remove these payloads if they were unprotected," said Michael Sailor, a professor of chemistry and biochemistry at UCSD who headed the team of chemists, biologists and engineers that turned the fanciful concept into reality. "These mother ships are only 50 nanometers in diameter, or 1,000 times smaller than the diameter of a human hair, and are equipped with an array of molecules on their surfaces that enable them to find and penetrate tumor cells in the body."

These microscopic cargo ships could one day provide the means to more effectively deliver toxic anti-cancer drugs to tumors in high concentrations without negatively impacting other parts of the body...

Investigators at the Translational Genomics Research Institute (TGen) today announced a faster and less expensive way for scientists to find which genes might affect human health.

Using bar-codes, not unlike what shoppers find in grocery stores, TGen researchers found a way to index portions of the nearly 3-billion-base human genetic code, making it easier for scientists to zero in on the regions most likely to show variations in genetic traits.

The findings were published today in the online version of the journal Nature Methods. The study will be published in print in the journal's October edition.

Dr. David Craig, associate director of TGen's Neurogenomics Division, said the new method should cost only one-tenth, or less, of the current cost of sequencing genes commonly done to analyze Single Nucleotide Polymorphisms (SNPs), and in performing Genome-Wide Association (GWA) studies.

"Our goal is to find the genetic basis of disease,'' said Craig, the study's lead author. "It (the new method) provides us a way to immediately use next-generation sequencing technology for studying hundreds to thousands of individuals.''

John Pearson, the head of TGen's Bioinformatics Research Unit, said the new method would allow scientists worldwide to more easily tune their sequencing experiments, and conduct their experiments with greater speed...

Selenium has been referred to as an "essential toxin" due to the fact that it shows only a marginal line between the nutritious requirement and toxic effects upon exposure. The steep dose response curve due to bioaccumulation effects have lead to the characterization of selenium as a "time bomb" that can be fused by exceeding a narrow threshold concentration in ecosystems through anthropogenic activities. Ironically, an estimated 0.5 to 1 billion people worldwide suffer from selenium deficiency, whereas areas of toxicity can be separated from selenium deficient areas by only 20 km.

The microbiological treatment of selenium - so called "dissimilatory metal reduction" - could supersede this problem, as selenium-reducing microorganisms are highly selective for selenate, reducing it to insoluble, less-toxic elemental selenium that can potentially be recovered from the process.

A study funded by the European Union, published in the September-October issue of the Journal of Environmental Quality, demonstrates that the biological treatment is indeed efficient for selenate reduction, and substantial amounts of selenate are converted to methylated selenium species or nano-sized elemental selenium particles. The emission of nano-sized selenium particles is problematic, as these can become bioavailable by direct assimilation or reoxidize to selenite and selenate. Dimethlyselenide and dimethyldiselenide, two species with unknown ecotoxicological long-term effects, contributed substantially to selenium dissolved in the effluent. Their formation was induced by minor temperature changes during biological reduction, thus a careful process control might drastically increase removal success of existing biotreatment systems for selenium and is a prerequisite for successful removal in full scale applications...

Unlike some parents, adult stem cells don't seem to mind when their daughters get a tattoo. In fact, they're willing to pass them along.

Using the molecular equivalent of a tattoo on DNA that adult stem cells (ASC) pass to their "daughter" cells in combination with gene expression profiles, University of Utah researchers have identified two early steps in adult stem cell differentiation—the process that determines whether cells will form muscle, neurons, skin, etc., in people and animals.

The U of U researchers, led by Alejandro Sanchez Alvarado, Ph.D., professor of neurobiology and anatomy, identified 259 genes that help defined the earliest steps in the differentiation of adult stem cells in planarians—tiny flatworms that have the uncanny ability to regenerate cells and may have much to teach about human stem cell biology.

The findings, reported in the Sept. 11 issue of Cell Stem Cell establish planarians as an excellent model for studying adult stem cells in a live animal, rather than a laboratory culture dish.

"This allows us to study an entire stem cell population in its own environment," said Sanchez Alvarado, also an investigator with the Howard Hughes Medical Institute and the study's senior author. "It's likely that what we learned here can be applied to our own stem cell biology."

Planarians share similar biology with humans in many ways. They also, for reasons unknown, regenerate cells unlike any other animal—an entirely new worm can form from just a fragment of another worm. Planarians constantly regenerate new cells to replace those that die naturally or from injury...

Researchers sequencing the DNA of blue-green algae found a linear chromosome harboring genes important for producing biofuels. Simultaneously analyzing the complement of proteins revealed more genes on the linear and the typical circular chromosomes then they'd have found with DNA sequencing alone.

The team recently reported the cyanobacterium Cyanothece 51142's genome in the Proceedings of the National Academy of Sciences Early Edition. Overlaying protein data let the researchers pinpoint about 16 percent more genes than by DNA sequencing alone. The collaboration included a proteomics team from the Department of Energy's Pacific Northwest National Laboratory, a gene sequencing team from the Washington University Genome Sequencing Center, and researchers from Washington University, Saint Louis University, and Purdue University.

"This is the first time anything like this has been found in photosynthetic bacteria. It's extremely rare for bacteria to have a linear chromosome," said team leader Himadri Pakrasi from WUSTL. "Nearly 100 percent of them do not."

Cyanobacteria are unique among bacteria because they seem part plant-like and part microbe-like. They use the sun's energy to make sugar via photosynthesis like plants do. And like bacteria, Cyanothece 51142 has other key life-sustaining functions, such as doctoring atmospheric nitrogen so other species can use it. This so-called nitrogen fixation is performed by a handful of bacterial species in water and soil. Cyanothece also makes ethanol and hydrogen, activities that drew the attention of the DOE and others looking for new ways to make fuel...

A new study suggests that bacteria-infecting viruses – called phages – can make collective decisions about whether to kill host cells immediately after infection or enter a latent state to remain within the host cell.

The research, published in the September 15 issue of the Biophysical Journal, shows that when multiple viruses infect a cell, this increases the number of viral genomes and therefore the overall level of viral gene expression. Changes in viral gene expression can have a dramatic nonlinear effect on gene networks that control whether viruses burst out of the host cell or enter a latent state.

"What has confounded the virology community for quite some time is the observation that the cell fate of a bacteria infected by a single virus can be dramatically different than that infected by two viruses," said Joshua Weitz, an assistant professor in the School of Biology at the Georgia Institute of Technology. "Our study suggests that viruses can collectively decide whether or not to kill a host, and that individual viruses 'talk' to each other as a result of interactions between viral genomes and viral proteins they direct the infected host to produce."

To study viral infections, Weitz teamed with postdoctoral fellow Yuriy Mileyko, graduate student Richard Joh and Eberhard Voit, who is a professor in the Wallace H. Coulter Department of Biomedical Engineering, the David D. Flanagan Chair Georgia Research Alliance Eminent Scholar in Biological Systems and director of the new Integrative BioSystems Institute at Georgia Tech....

Researchers have developed a clever method to purify parasitic organisms from their host cells, which will allow for more detailed proteomic studies and a deeper insight into the biology of organisms that cause millions of cases of disease each year.

Many infectious pathogens, like those that cause Toxoplasmosis or Leishmaniases, have a complex life cycle alternating between free-living creature and cell-enclosed parasite. A thorough analysis of the proteins that help these organisms undergo this lifestyle change would be tremendously useful for drug or vaccine development; however, it's extremely difficult to separate the parasites from their host cell for detailed study.

As reported in the September Molecular & Cellular Proteomics, Toni Aebischer and colleagues worked around this problem by designing special fluorescent Leishmania mexicana (one of the many Leishmaniases parasites). They then passed infected cells through a machine that can separate cell components based on how much they glow. Using this approach, the researchers separated the Leishmania parasites with only about 2% contamination, far better than current methods...